Z axis alignment for perpendicular

How do you make adjustments on the gantry to square up the z axis? When skimming a 1/4" flat end mill over a painted surface only 1/2 of the bit is removing paint while the other half is not. My spoilboard is milled to be perfectly level with the machine. The misaligned z axis also causes a lot of problems in the 5 and/or 7 o’clock position when trying to cut circles. It binds causing missed steps. I’m using a 400 watt 48v spindle moving at 10mm/s at .5mm depths per cut. Anything faster on a curve and it ruins the project.

I have the same question. I just finished my whole setup here. It helps to change the tension of the bolts that hold the bearings for the z conduit a little. Experiment a little. It is hard to get just right. I am pretty close on my x axis but my y axis perpendicularity is terrible. I check with a small square and a 1/8 drill bit on the collet running to the spoilboard. Make sure all your bearings are making good contact with the conduit, and check the z axis for torsion by placing it on a flat surface.

I thought I saw Ryan replied to this? Anyway, print yourself one of these. https://www.thingiverse.com/thing:1525661 Mount on your router. Use duct tape or masking tape as shim stock.